Re: [AMBER] Terminal phosphates with RNA

From: David A Case via AMBER <>
Date: Wed, 22 Feb 2023 10:14:59 -0500

On Wed, Feb 22, 2023, Piia Bartos via AMBER wrote:
>I am trying to simulate an RNA-protein complex where I need the parameters
>for 5' terminal phosphates. I know of terminal_monophosphate.lib and
>terminalphos.LJbb-RNA.lib, which should contain these parameters for the
>corresponding force fields.
>The problem is that these simulations crash because of the phosphates
>become unstable, after a few ns of the production run. My default settings
>include ff19SB for protein, OL3 for RNA and OPC water model, and HMR to use
>4fs timestep.

Can you say what you mean by "the phosphates become unstable"? Are close
contacts formed between the terminal phosphate and some other group?

I don't think there is any fundamental problem with the paramters -- I have
run many simulations that appeared to be fine. But that doesn't mean that
these parameters are always good. You need to find out what is going wrong
-- a simple visualization of the trajectory is the best first step. If the
problem involves the protein, that is probably very system-dependent.
One point: be sure that you system really has a single phosphate at the 5'
terminus, and you are not just trying to simulate what some crystallographer


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Received on Wed Feb 22 2023 - 07:30:02 PST
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